I am using Linux Driver 1.0-4496 in hardware stereo mode. Some applications (VMD, O) appear to erratically exchange the left and right image after some minutes of usage. This is perceived as an irritating exchange of front and rear. I never observed this strange effect using W2K as operating System on the same machine. Any clue?

You may want to set the environment variable __GL_SYNC_TO_VBLANK to something (with setenv in CShell).
As mentioned in the README file of the driver, this "forces glXSwapBuffers to synchronize to your monitor's vertical refresh rate".

I encountered exactly the same problem that you described and this greatly enhanced operations (Quadro4 750 XGL, RedHat 9, driver 1.0-4363). Users now tell me that during their 2-3 hours sessions the rear-front inversion doesn't happen at all, when myself, still was able to find one inversion after approx. 15mn of molecular manipulation. Anyway, this is nothing compared with the inversionss that happened every 10-15s or so, before. Also, I have the impression that reducing the V rate to 100Hz or so would not hurt, in this context.